Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005842.1 Hibiscus syriacus cultivar Beakdansim tig00013706_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 197362
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 2 of 2
Found at i:179475 original size:15 final size:15
Alignment explanation
Indices: 179394--179489 Score: 59
Period size: 16 Copynumber: 6.0 Consensus size: 15
179384 TTCACTTTCG
* *
179394 TTTCTTCTTCTATTT
1 TTTCTTCTTTTCTTT
*
179409 TCTCTT-TGTTTCTTT
1 TTTCTTCT-TTTCTTT
* *
179424 TTCTTTTCATTTCATTT
1 TT-TCTTCTTTTC-TTT
*
179441 TCCTTCTTTCCTTTCTTT
1 T--TTC-TTCTTTTCTTT
*
179459 TTTTTTCTTTTACTTT
1 TTTCTTCTTTT-CTTT
179475 TTTCTTCTTTTCTTT
1 TTTCTTCTTTTCTTT
179490 CACTTTTTCT
Statistics
Matches: 62, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
14 1 0.02
15 21 0.34
16 23 0.37
17 4 0.06
18 5 0.08
19 8 0.13
ACGTcount: A:0.04, C:0.21, G:0.01, T:0.74
Consensus pattern (15 bp):
TTTCTTCTTTTCTTT
Found at i:179487 original size:21 final size:20
Alignment explanation
Indices: 179444--179503 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
179434 TTCATTTTCC
*
179444 TTCTTTC-CTTTCTT-TTTTT
1 TTCTTTCACTTT-TTCTTCTT
*
179463 TTCTTTTACTTTTTTCTTCTT
1 TTCTTTCAC-TTTTTCTTCTT
179484 TTCTTTCACTTTTTCTTCTT
1 TTCTTTCACTTTTTCTTCTT
179504 CATCAGCAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 6 0.17
20 14 0.40
21 15 0.43
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (20 bp):
TTCTTTCACTTTTTCTTCTT
Found at i:180200 original size:7 final size:7
Alignment explanation
Indices: 180184--180275 Score: 64
Period size: 7 Copynumber: 13.1 Consensus size: 7
180174 TTCATTTTCC
180184 TTTC-TT
1 TTTCTTT
180190 TTTCTTT
1 TTTCTTT
*
180197 TTTCTCAT
1 TTTCT-TT
180205 TTTC-TT
1 TTTCTTT
180211 TTTCTTT
1 TTTCTTT
180218 TTTCTATT
1 TTTCT-TT
*
180226 TTCCTTT
1 TTTCTTT
*
180233 TATCTCTT
1 TTTCT-TT
*
180241 TTTATTT
1 TTTCTTT
* *
180248 TTCCCTT
1 TTTCTTT
*
180255 TTTC-CT
1 TTTCTTT
*
180261 TTCCTTT
1 TTTCTTT
180268 TTTCTTT
1 TTTCTTT
180275 T
1 T
180276 CTTTTCTGGA
Statistics
Matches: 65, Mismatches: 15, Indels: 11
0.71 0.16 0.12
Matches are distributed among these distances:
6 13 0.20
7 36 0.55
8 16 0.25
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTCTTT
Found at i:180209 original size:21 final size:20
Alignment explanation
Indices: 180184--180248 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 20
180174 TTCATTTTCC
180184 TTTCTTTTTCTTTTTTCTCAT
1 TTTCTTTTTCTTTTTTCT-AT
180205 TTTCTTTTTCTTTTTTCTAT
1 TTTCTTTTTCTTTTTTCTAT
*
180225 TTTCCTTTTATCTCTTTT-TAT
1 TTT-CTTTT-TCTTTTTTCTAT
180246 TTT
1 TTT
180249 TCCCTTTTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
20 5 0.12
21 29 0.71
22 7 0.17
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTCTTTTTCTTTTTTCTAT
Found at i:180220 original size:13 final size:13
Alignment explanation
Indices: 180184--180280 Score: 72
Period size: 15 Copynumber: 7.1 Consensus size: 13
180174 TTCATTTTCC
180184 TTTCTTTTTCTTT
1 TTTCTTTTTCTTT
180197 TTTCTCATTTTC-TT
1 TTTCT--TTTTCTTT
180211 TTTCTTTTTTCTATT
1 TTTC-TTTTTCT-TT
*
180226 TTCCTTTTATCTCTT
1 TTTCTTTT-TCT-TT
* *
180241 TTTATTTTTCCCTT
1 TTTCTTTTT-CTTT
* *
180255 TTTCCTTTCCTTT
1 TTTCTTTTTCTTT
180268 TTTC-TTTTCTTT
1 TTTCTTTTTCTTT
180280 T
1 T
180281 CTGGATAGAA
Statistics
Matches: 67, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
12 8 0.12
13 17 0.25
14 19 0.28
15 23 0.34
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTCTTTTTCTTT
Found at i:187356 original size:16 final size:16
Alignment explanation
Indices: 187335--187368 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
187325 AAAAGTTTTA
187335 ATAAATG-AATATAAAT
1 ATAAATGTAA-ATAAAT
187351 ATAAATGTAAATAAAT
1 ATAAATGTAAATAAAT
187367 AT
1 AT
187369 TAACACAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (16 bp):
ATAAATGTAAATAAAT
Found at i:191936 original size:26 final size:23
Alignment explanation
Indices: 191892--191943 Score: 59
Period size: 26 Copynumber: 2.1 Consensus size: 23
191882 CTATCATGCA
*
191892 ATTATTATTTATAACATGCTATT
1 ATTATTATTTATAACATGCAATT
*
191915 ATTATTATTATCTAACATATGCAATT
1 ATTATTATT-TATAAC--ATGCAATT
191941 ATT
1 ATT
191944 TAATACCTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 9 0.38
24 5 0.21
26 10 0.42
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.50
Consensus pattern (23 bp):
ATTATTATTTATAACATGCAATT
Found at i:192216 original size:51 final size:52
Alignment explanation
Indices: 192156--192296 Score: 185
Period size: 54 Copynumber: 2.7 Consensus size: 52
192146 CAAACGAACA
* * * *
192156 CTAGAGCTTACTCGATCTTAAAAATTTGCTCTA-CTCCATAAAAAAGGAATT
1 CTAGAGCTTATTCGGTCTTAGAAATTTGCTCTACCTCCATAAAAAAGGAATG
*
192207 CTAGAGCTTATTCGGTCTTAGAAATTTTCTCTACTCCTCCATAAAAAAGGAATG
1 CTAGAGCTTATTCGGTCTTAGAAATTTGCTCTA--CCTCCATAAAAAAGGAATG
* * *
192261 CTAGAGCATGTTCGGTCTTAGAAATTTGCTTTACCT
1 CTAGAGCTTATTCGGTCTTAGAAATTTGCTCTACCT
192297 ATCGTTAGTA
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
51 29 0.37
52 3 0.04
54 46 0.59
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (52 bp):
CTAGAGCTTATTCGGTCTTAGAAATTTGCTCTACCTCCATAAAAAAGGAATG
Done.